Tag Archives: gene regulatory networks

Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network ...

Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. Here a team led by ...

Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a ...

The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of each cell. Such analyses can reveal detailed expression dynamics and functional relationships for differentiation. To further ...

Developing blood cells are caught in tugs of war between competing gene regulatory networks before finally deciding what type of cell to become, according to a study published Aug. 31 in Nature. Researchers at Cincinnati Children’s Hospital Medical Center report ...

Systems biology is a research area which aims to understand living systems as a whole, instead of focusing on single biological entities. Gene regulatory network inference is a systems biology approach which predicts interactions between genes with the help of ...

Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). Both the experimental setup and the nature of PHIs exhibit certain characteristics. First, besides an environmental change, the battle ...